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- PDB-1jmv: Structure of Haemophylus influenzae Universal Stress Protein At 1... -

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Basic information

Entry
Database: PDB / ID: 1jmv
TitleStructure of Haemophylus influenzae Universal Stress Protein At 1.85A Resolution
ComponentsUniversal Stress Protein A
KeywordsCHAPERONE / universal stress protein / uspa
Function / homology
Function and homology information


Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Universal stress protein A homolog
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsSousa, M.C. / McKay, D.B.
CitationJournal: Structure / Year: 2001
Title: Structure of the universal stress protein of Haemophilus influenzae.
Authors: Sousa, M.C. / McKay, D.B.
History
DepositionJul 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Universal Stress Protein A
B: Universal Stress Protein A
C: Universal Stress Protein A
D: Universal Stress Protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4888
Polymers63,1044
Non-polymers3844
Water3,819212
1
A: Universal Stress Protein A
B: Universal Stress Protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7444
Polymers31,5522
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-50 kcal/mol
Surface area12940 Å2
MethodPISA
2
C: Universal Stress Protein A
D: Universal Stress Protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7444
Polymers31,5522
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-50 kcal/mol
Surface area12150 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-111 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.129, 63.214, 136.959
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. The asymmetric unit conyains 2 dimers

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Components

#1: Protein
Universal Stress Protein A / uspA


Mass: 15776.032 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: USPA / Plasmid: pTYB2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P44880
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 400, sodium cacodylate, ammonium sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-10 mg/mlprotein1drop
221 %PEG40001reservoir
3200 mMammonium sulfate1reservoir
4100 mMsodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 49842 / Num. obs: 49785 / % possible obs: 99.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 29.4
Reflection shellResolution: 1.85→1.91 Å / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 14.4 / Rsym value: 0.103 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 339160
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→28.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2704063.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2895 5.8 %RANDOM
Rwork0.22 ---
all-49714 --
obs-49714 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.8378 Å2 / ksol: 0.354021 e/Å3
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1--8.11 Å20 Å20 Å2
2--17.64 Å20 Å2
3----9.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.85→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 20 212 4318
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 421 5.1 %
Rwork0.24 7755 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 46819 / σ(F): 0 / % reflection Rfree: 5.8 % / Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.282 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.24 / Rfactor obs: 0.24

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